We evaluated self-assembled monolayers (SAMs) as potential coatings to prevent bacterial adhesion to biomaterials. Bacterial retention experiments were conducted on SAMs, some of which were coated with the model proteins fetal bovine serum (FBS) and fibronectin (FN). A thermodynamic approach was applied to calculate the Gibbs free energy changes of adhesion (Delta G(adh)) of Staphylococcus epidermidis interacting with the substrates. When only nonspecific interactions controlled bacterial attachment, such as for the non-protein-coated substrates or the FBS substrates, the correlation between the thermodynamic predictions and measured values of bacterial retention was strong. However, when FN was adsorbed to the surfaces, the thermodynamic modeling underestimated bacterial adhesion, presumably since specific interactions between proteins of S. epidermidis and FN led to stronger attachment. Bacterial viability on the substrates was correlated with thermodynamic properties. For example, although bacteria attached more to surfaces having negative Delta G(adh) values, these cells experienced the greatest loss of viability, presumably since strongly attached bacteria were unable to divide and grow. When the Delta G(adh) values were decoupled into their components, we saw that acid-base interactions due to hydrogen bonding dominated the interactions of bacteria and proteins with each other and with the substrates in aqueous media. Finally, we discuss concerns regarding the use of the thermodynamic model to predict bacterial adhesion behavior in biomaterials systems.